Research workbench
Crystal structure of thermus thermophilus transhydrogenase heterotrimeric complex of the ALPHA1 subunit dimer with the NADP binding domain (domain III) of the beta subunit
Analyse Crystal structure of thermus thermophilus transhydrogenase heterotrimeric… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J16
- Type
- protein
- Length
- 918 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD/NADP transhydrogenase alpha subunit 1; NAD(P) transhydrogenase subunit beta
- EC
- 1.6.1.2
- UniProt
- Q72GR8, Q72GS0
- Ligands
- NAD, NAP, CL
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD/NADP transhydrogenase alpha subunit 1 (EC 1.6.1.2) | protein | 372 | 38% helix, 19% strand | Q72GR8 |
| B | NAD/NADP transhydrogenase alpha subunit 1 (EC 1.6.1.2) | protein | 369 | 37% helix, 19% strand | Q72GR8 |
| C | NAD(P) transhydrogenase subunit beta (EC 1.6.1.2) | protein | 177 | 43% helix, 18% strand | Q72GS0 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains A, C
- CL · Chloride ion · ion · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B, C
- PGE · Triethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1057 | 0.82 | 0.83 | 121 | NAD, NAP |
| 2 | 932 | 0.76 | 0.79 | 69 | NAD, PGE |
| 3 | 173 | 0.47 | 0.76 | 26 | GOL |
| 4 | 184 | 0.46 | 0.75 | 30 | empty |
| 5 | 125 | 0.40 | 0.75 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1945 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 725 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 437 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4J16 · Crystal structure of Thermus thermophilus transhydrogenase heterotrimeric complex of the… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q72GR8
- Every structure of UniProt Q72GS0
- Elsewhere: RCSB PDB 4J16 · PDBe 4J16 · UniProt Q72GR8 · UniProt Q72GS0
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